Notes:
TO ADD OR REMOVE A BUTTON YOU CAN EITHER HAVE THE MOUSE CURSOR OVER THE BUTTON TO BE REMOVED WHEN YOU EXECUTE /MBF ADD OR /MBF REMOVE OR YOU CAN NOW TYPE IN THE NAME OF THE BUTTON. /MBF ADD [ButtonName] OR /MBF REMOVE [buttonName]
The ability to add minimap icons to the table can be a general or partial name of the icons. The button override table add should be the exact name of the button that you want to override and collect.

PLEASE MAKE SURE THAT YOU UPDATE ACE 3 TO THE LATEST VERSION IF YOU HAVE IT INSTALLED AS A SEPARATE ADDON

I never had the problem before patch. The problematic buttons in my case, are Atlasloot, Bartender4, Bigwigs, Skada, Professionsvault and Bugsack. It happends very random. Sometimes the black layer is gone when logging in, sometimes not.

I use Shadowed Unit Frames for the UI.

I found out, that if I via MBF display - buttonskin choose another skin, then all buttons turn visible again, but as soon as I reload UI, the black icons return.

This is currently stealing the Blizzard Queueing Interface for LFR/LFR/PVP map button from the minimap and has no option to place it back. Please add one or let us know how to manually set it as an exception.